[NMR paper] Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related ArticlesLysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
Biochemistry. 2018 Apr 17;:
Authors: Baird-Titus JM, Thapa M, Doerdelmann T, Combs KA, Rance M
Abstract
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics, and may therefore play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues. We report on studies of a model system, the homeodomain-DNA complex, focusing on the Lys50 class of homeodomains where a key lysine residue in position 50 was shown previously to be critical for binding site specificity. NMR methodology was employed for determining the dynamics of lysine side-chain amino groups via 15N relaxation measurements in the Lys50-class homeodomains from the Drosophila protein Bicoid and the human protein Pitx2. In the case of Pitx2, complexes with both a consensus and a non-consensus DNA binding site were examined. NMR-derived order parameters indicated moderate to substantial conformational freedom for the lysine NH3+ group in the complexes studied. To complement the experimental NMR measurements, molecular dynamics simulations were performed for the consensus complexes to gain further, detailed insights regarding the dynamics of the Lys50 side chain and other important residues in the protein-DNA interface.
PMID: 29664630 [PubMed - as supplied by publisher]
[NMR paper] Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Biochemistry. 2018 Feb 07;:
Authors: Solomentsev G, Diehl C, Akke M
Abstract
FKBP12 (FK506 binding protein 12 kDa) is an important drug target that attracts a great deal of interest as a model system for computational drug design and studies on the role of protein dynamics in ligand binding. NMR...
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NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
Publication date: 2 February 2018
Source:Biophysical Journal, Volume 114, Issue 3, Supplement 1</br>
Author(s): Falk Hoffmann, Mengjun Xue, Frans Mulder, Lars Schäfer</br>
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[NMR paper] Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy.
Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy.
Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy.
Chemistry. 2015 Jun 12;
Authors: Ivanir-Dabora H, Nimerovsky E, Madhu PK, Goldbourt A
Abstract
Magic-angle spinning solid-state NMR spectroscopy has been applied to study the dynamics of CBM3b-Cbh9A from Clostridium thermocellum...
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06-16-2015 07:24 PM
[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
J Phys Chem B. 2014 Oct 28;
Authors: Allnér O, Foloppe N, Nilsson L
Abstract
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...
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10-29-2014 03:51 PM
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.
Biochim Biophys Acta. 2011 Aug;1808(8):2019-30
Authors: Romo TD, Bradney LA, Greathouse DV, Grossfield A
Abstract
One approach to the growing health problem of antibiotic resistant bacteria is the development of antimicrobial peptides (AMPs) as alternative treatments. The...
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08-19-2011 02:56 PM
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
J Am Chem Soc. 2010 Dec 27;
Authors: Esadze A, Li DW, Wang T, Bru?schweiler R, Iwahara J
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics...
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Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear 1H-15N NMR Spectroscopy
Alexandre Esadze, Da-Wei Li, Tianzhi Wang, Rafael Bru?schweiler and Junji Iwahara
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107847d/aop/images/medium/ja-2010-07847d_0007.gif
Journal of the American Chemical Society
DOI: 10.1021/ja107847d
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/iFwgRBt-zto
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[NMR paper] Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studi
Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Related Articles Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
Biochemistry. 2001 Jun 5;40(22):6559-69
Authors: Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ
A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is...
Lysine Side-Chain Dynamics in the Binding Site of Homeodomain/DNA Complexes as Observed by NMR Relaxation Experiments and Molecular Dynamics Simulations.
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